Transformers Prime meets Thomas and Friends
by Kingstriker
Summary: Transformers Prime/Thomas and friends. When Starscream is spotted on the Island of Sodor, the Autobots go to look for him. But when the Decepticons go there to look for energon, will the autobots have to give up their cover to save the island?
1. Chapter 1: The Island

Transformers Prime meets Thomas and Friends

_**Yes, I admit it. I am also a huge Thomas and Friends fan just as much as I am a Transformers fan. If you have no idea what Thomas is, or you do but don't watch it. Then you shouldn't read this. **_

Chapter 1: The Island

The Autobot base was quiet today. Nothing to research on, nowhere to go, nothing much to say. Optimus and Ratchet were actually trying out watching TV with Jack, Miko and Raf. Bee and Bulkhead were playing basketball by way of Cybertron. Arcee was the referee.

"I wish there was something better to do!" Miko said flipping through channels.

"Yeah, are you sure there are not any energon-filled locations?" Jack asked nearly falling asleep.

"If there was, don't you think I would have been at the monitor checking right now?" Ratchet grumbled.

"Whatever!" Miko said.

_**Meanwhile on the Nemesis...**_

Even the decepticons were bored. All the eradicons were lying around, Megatron zoning out on his chair, Soundwave watching Youtube videos on his faceplate screen, Knock Out digging his claws in his medical desk, Breakdown was asleep, Airachnid was away looking around the planet. Starscream was gone at this point to who knows where. Megatron wanted to hunt him down and kill him for betraying the decepticons.

"Since when could being evil be so boring?" Knock Out said to his assistant who was still sleeping.

"How could I possibly be tired and bored?" Megatron thought to himself before accidenly zoning out again. "Starscream always made this place fun. All the beatings and torture I give him sure kept me going! Where is that traitor?"

_**Meanwhile on the Island of Sodor...**_

Thomas had just been given the job to take passengers around the island. He was eager to get out the shed. He found Annie and Clarabel and proceeded to get the passengers. Later at one of the water tanks, Percy came by looking afraid.

"What's wrong Percy?" Thomas asked.

"Thomas, I saw something really strange in the sky. It was grey and very fast and I thought I heard it talk." Percy explained.

Just then they were interupted by Gordon who was pulling the express.

"Oh please Percy, you and your imaginations" Gordon wheeshed as he sped by.

"I'm telling the truth!" Percy said.

"I believe you Percy! Mabye we should look for it, but I have a job to do!" Thomas said and puffed away.

"A grey and fast object!" Thomas thought to himself. "I wonder what or who it could be!"

_**Meanwhile back at the Autobot Base...**_

Raf, Jack and Miko were watching TV. Bee and Arcee happened to come over and see what they were watching.

"Who's that little blue engine?" Arcee said pointing the engine going by the screen.

"Oh that's Thomas. This show is a classic. All about him and his friends out on adventure around an Island." Raf said.

Bee buzzed with curiosity at the characters and environment.

"Who would ever want to waste time making a show like that?" Ratchet said who glared at the TV. "Their faces aren't even moving!"

"RATCHET!" Arcee snapped.

"Ratchet be nice!" Optimus said coming into the room. "I may not be a fan of Television but I do find some of its programs a little interesting."

"It's early in the day, they show the old model train version in the morning, then later in the day they show it in CGI." Jack explained.

"If only the Island of Sodor really existed." Miko said. "Unless...could it possibly be hidden somehow from other's eyes. Mabye like it can only be accesed by mabye another demension?" she added getting excited.

"Possibly!" Optimus said.

"Optimus, the decepticons had not caused any activity for at least 2 months. Would it bother to take a little vacation?" Jack asked.

"Perhaps not, the decepticons have been very quiet lately. I'm sure it wouldn't hurt." Optimus said seeing a smile on the humans faces. "Ratchet find coordinates of this "Island of Sodor".

Ratchet wanted to protest but instead he said nothing. He looked around to see if the place existed. Suddenly he recieved the location along with an unidentified seeker roaming around it.

"Optimus, the location had been found but a seeker has been living among them!" Ratchet said as Optimus took a look.

"THE PLACE EXISTS, YES, YES, YES!" Miko shouted out loud.

"QUIET!" Ratchet demanded. "Judging by the figure of this seeker, this must be Starscream. But what is Starscream doing there?"

"Unless energon exists there and the engines are not aware of it at all!" Bulkhead said.

"Autobots, apparently this will be no vacation, instead, it is a spying mission to see what Starscream is up to." Optimus explained much to the dissapointment of Bee and the humans.

"We must remain in vehicle mode for as long as possible!" Optimus continued.

"But how are we going to get there? The groundbridge can't take us to another demension." Raf said.

Then everyone turned to the TV which still had the show on.

Bee buzzed and clicked his idea much to the dissaproval of Ratchet.

"Bumblebee, you can't just connect the TV to the groundbridge controls and automaticaly transport us there!" Ratchet scoffed.

However, Miko had already brought the TV over near the controls.

"Ratchet, it's worth a shot!" Arcee said helping to connect the TV. "It's possibly our only chance."

Suddenly the groundbridge activated by itself leaving Ratchet's mouth wide open.

"COME ON HURRY! Miko said already running for it. Jack and Raf followed as the autobots (Except Ratchet) transformed and zoomed away.

**_Meanwhile on the Nemesis..._**

An alarm came on waking Megatron up from a little nap he was having.

"Soundwave what's going on?" Megatron said coming over to the TIC.

Soundwave pointed out coordinates the autobots have used. Just then, Breakdown and Knock Out came in wondering what all the noise was.

"What are the autobots up to?" Knock Out asked.

"Finally some action!" Breakdown said.

"What is the "Island of Sodor"? Megatron asked.

Soundwave's faceplate screen showed a video of Thomas and Percy riding around talking.

"Oh that show, I actually like it!" Knock Out said with Breakdown making a "WTF?" look!

"But how did they get there?" Megatron asked.

Soundwave, for the first time ever, shrugged meaning he didn't know!

"Mabye another demension!" Breakdown said. "I actually looked at a globe of the Earth and there is no "Island of Sodor" on it."

"You're right!" Megatron said. "Luckily we know a certain someone who can take you guys there!" Megatron said.

"Why are we going?" Breakdown asked.

"Why else would Optimus want to go there? To find energon!" Megatron said with a devilish smirk!

"Soundwave? You don't want to go?" Breakdown asked.

Soundwave shook his head no! But secretly he really did. He was secretly a fan of Percy! He unleashed a groundbridge from his faceplate screen and Knock Out and Breakdown jumped in. Once they were gone, Soundwave walked quickly out of the room. Megatron was puzzled.

"Soundwave, I know I'm not the type to say this but, are you okay?"

Soundwave stopped, looked back and shook his head yes. But inside he was dissapointed of why he didn't take the chance to go. He walked back to his berth and didn't even look at the eradicons that saw him. He sat on his berth and searched for "Thomas and Friends" on his faceplate screen.

_**To be continued...**_

_**I have always wanted to mixed these two shows together. Please tell me what you thought and no bad comments.**_


	2. Chapter 2: Blending In

Chapter 2: Blending In

_**On Island of Sodor...**_

As Team Prime arrived they realized they had arrived behind Tidmoth Sheds. Miko could barely contain how excited she was. Raf and Jack were amazed. The Autobots were also amazed.

"Wow, it really is CGI!" Raf said.

"Which means the engines have moving faces!" Miko said.

"Autobots, blend in and roll out!" Optimus commanded as they quietly snuck to the side of the sheds. They listened to the others conversations.

"Percy said he saw some alien-like ship in the sky" James said.

"What's an alien?" Henry asked worried.

"I don't know, but it sounds dangerous!" Edward said.

"Alien ship?" Arcee said moving out a little bit.

"Must be Starscream!" Bulkhead said.

"Did you here something?" Emily said puffing out the shed a bit.

"Autobots, fall back quietly." Optimus said as quietly as he could.

The Autobots backed up, turned around and headed for the nearest road to get on. Meanwhile Thomas was still taking passengers around the island. He was still thinking about what Percy had saw. He was so deep into thought he didn't notice Starscream hiding behind a large bush. Starscream couldn't believe what he just saw.

"A train with a face? A living train? This island must be full of them besides earthlings!" Starscream said.

He decided to follow Thomas. He transformed and flew above him making sure Annie and Clarabel didn't see him. Starscream considered this interesting. He wasn't going to terrorize the engines, but mabye try to befriend them so he wouldn't be attacked. What he didn't realize was Team Prime, Knock Out and Breakdown were on the island too. Thomas was racing down the track. But he wasn't in a hurry. Starscream thought Thomas knew he was above him but he risked it anyway. Suddenly Starscream saw a green engine about to go the opposite direction Thomas was going. Starscream quickly made a U-turn but it was too late.

"There it is again!" Percy said and went faster to catch up. "HEY! WHY ARE YOU RUNNING AWAY?"

Starscream knew his cover was blown and didn't want Percy to be suspicous the whole time. He hid right back where the large bush was. Percy screeched to a halt. It was silent for a moment. Starscream had transformed to robot mode and was trying not to make any noise. He could sense Percy's presence right on the other side of the bush.

"I'm sorry if I scared you! A lot of people say you are an alien, even I did. It's okay if you are but don't be afraid." Percy assured.

It was silent again. Starscream realized Percy wasn't going to go away till he revealed himself. So, Starscream gave up.

"Is there mabye, any place we can talk in private?" Starscream asked in a low voice.

"Sure, the smelters yard would be perfect! If you knew what that was!" Percy said.

"Oh I saw a map of the place, I know where to go from here! I will meet you there!" Starscream said revealing himself by flying away.

Percy watched as the seeker flew out of his distance. He began to head to the smelters yard and tried not to attract attention. Meanwhile Breakdown and Knock Out arrived, transformed and looked around a little impressed.

"Just like I see it on TV!" Knock Out said happily. "Well, the CGI episodes."

"What's so special about a place of talking trains?" Breakdown asked.

Knock Out turned to him with a "Shut up" look on his face.

"Screw looking for energon, I'm going exploring! Coming?" Knock Out asked his bulky assistant.

"Nah, you go your own way!" Breakdown said transforming and raced away.

"Suit yourself!" Knock Out said as he also transformed and went to look around.

Breakdown raced down a road to where Bertie was waiting at a crossing. Breakdown didn't say a thing as he stopped behind Bertie. Bertie could sense someone bigger than him behind him but he didn't say anything. Just then Gordon rolled through the crossing pulling the express. Breakdown looked at the long line of coaches. He was a little surprised. Knock Out was happy as he recieved cheering from children by his paintwork. He soon was heading down near James who was pulling coal trucks. James wasn't happy about it.

"I got to admit, James has some very nice paint. Sadly I can't tell him!" Knock Out said rolling up to the side of James.

Just then Spencer zoomed by knocking little rocks on to James and Knock Out.

"WATCH THE PAINT!" James and Knock Out yelled at the same time. Suddenly James looked over to Knock Out. Knock Out remained as quiet as he could as he rolled away faster.

"SCRAP!" He thought taking another road away from the puzzeled James.

Team Prime was still looking around for Starscream while also checking up on the engines. Optimus spied on Thomas and Edward. Bee and Raf spied on Toby. Arcee and Jack had Emily, and Bulkhead and Miko had Gordon and Henry. Optimus had aquired a map of the island and was impressed by their features and locations. Meanwhile at the smelters yard Percy had arrived and saw that the seeker had went inside to transform. Percy waited not even a bit scared.

"What is your name?" Starscream asked from inside the glowing red opening of the smelters.

"Percy!" he said happily. "What about you?"

"I am Starscream!" he said still inside.

"Starscream? That's a nice name!" Percy said puffing a bit closer. "So why are you here?"

Starscream knew he had to lie, he didn't want anyone else to know about the war. So he decided to lie but tell some truths first.

"I come from a different planet, a planet called Cybertron. It's full of robotic organisms that have the abilty to scan any Earth vehicle and transform into it. That jet you saw was not really my true form." Starscream explained.

Percy was amazed. Then Starscream lied next.

"I am here on this planet to look for useful parts and devices to take back to Cybertron. However, we can never be seen. But, you saw me so I have no choice. But you can't tell anyone that you met me." Starscream said. He was really looking for energon.

"But what about Thomas? He's curious too! He's looking for you!" Percy said.

"Fine, tell him, but no one else. I won't be here for long. When I'm gone, you must forget about all of this!" Starscream said.

"I promise. So can I see you?" Percy asked backing up a bit.

Starscream gulped but took one step forward, and another. Percy's eyes went wide as standing before him was a tall, red-eyed, long-clawed, big heeled, big-winged robot. Percy was silent as he stared up at the mech. Starscream saw before him a little green engine.

"Wow, a real alien!" Percy said.

Starscream thought Percy was actually kind of cute. He knelt down to get a better look at the engine.

"So, tell me about yourself?" Starscream asked.

Meanwhile, Thomas was racing down the track with a now empty Annie and Clarabel. He was now trying to find Percy. Optimus was keeping a close watch on him making sure he was not going to be attacked by Starscream.

"Those numbers on their sides must mean something!" Optimus said noticing the number 1 on Thomas. "Was he the first one ever made perhaps?" he thought to himself.

_**NOTE: Every person reading this should face-palm right now because apparently Optimus didn't do any research on engine number identification.**_

Bee, in vehicle mode, and Raf watched as Toby rolled along the rails with Henrietta towards the quarry. Bee buzzed with confusion of why he looked different.

"He's a tram engine, all tram engines have cowcatchers all around them. I think they are cool!" Raf said.

Over near Knapford station, Gordon and Henry were talking. Miko and Bulkhead, in vehicle mode, were spying.

"I bet if you were a train, you could pull way more coaches than he can!" Miko said.

"Nah, Gordon seems like he can pull more than what he's pulling. But I don't know about Henry!" Bulkhead said seeing Gordon puff away pulling 6 coaches.

Jack and Acree watched as Emily was sleeping at Tidmoth sheds. Edward came by looking tired from doing his work.

"Wow, he really is tired, for an old engine!" Acree said. "He looks like Thomas in the future."

"Uh Arcee, engines don't grow, they are made that same size. Thomas would never be the next Edward." Jack laughed. "I wonder where Sir Topham Hatt is-OH NO!" Jack screamed seeing STH's car coming near them. Luckily Arcee was still a motorcycle. STH parked his car right beside them and he noticed Jack.

"Good day young man!" STH said walking past him.

"Good day sir, nice day isn't it?" Jack asked a little embarrased.

"It sure is! Nice motorcycle!" STH said as he hopped on the tracks leading to Edward.

"Thank you sir!" Jack said getting on Arcee. Arcee was about to laugh loudly.

"SHH!" Jack said as they sped away.

Meanwhile at the smelters, Percy and Starscream were just finishing off a conversation.

"Well Percy I got to go scan around this place, say, there isn't a scap yard near here is there?" Starscream asked with a smirk on his face.

"Well, usually I can never get a good look from here!" Percy said sadly.

Starscream wasn't phazed the least. He actually picked up Percy, much to his surprisement, and placed Percy high in the air.

"Can you see now?" Starscream asked.

Percy looked all around and smiled.

"Yeah just over there!" Percy said.

"Thanks!" Starscream said putting Percy down carefully on the track.

"Yeah, no problem, I got to go too in case STH has something else for me to do." Percy said backing up.

"Alright see you around and remember what I said." Starscream said before transforming right before Percy's eyes. "Oh, tell Thomas that I will see him at some point" Starscream said and flew away into the sky leaving Percy in awe. Percy went back to Tidmoth Sheds. Breakdown was hiding in the quarry throwing and smashing rocks around having fun. Suddenly he got a reading on energon near his location. He spotted a whole pile of Energon rocks that were disquised as regular rocks. He contacted Megatron.

"Lord Megatron I have aquired a large amount of energon!" Breakdown said making sure no one was around.

_**On the Nemesis...**_

"Excellent Breakdown, but keep looking we must try to aquire as much as possible, I will send a secret groundbridge." Megatron said.

"Okay, and tell Soundwave he's missing a good time." Breakdown said.

"Uh-" Megatron studdered at the thought. His TIC had not come from his room for a long time. "That probably isn't the best thing to do right now Breakdown!" Megatron said as the groundbridge revealed Breakdown coming with the energon rocks.

"There you go, fresh from the Island of Sodor!" Breakdown said.

"What about Knock Out?" Megatron asked.

"He's probably still looking!" Breakdown said going back through.

_**Back on Sodor...**_

However, Knock Out wasn't looking, he was enjoying himself. He had forgotton the whole reason they were there.

_**Again on the Nemesis...**_

Soundwave was in his room reading when Megatron knocked on his door. Never once had Megatron been worried for somebody. Soundwave opened it to see his Commander with a concerned look.

"Soundwave, you haven't came out in a long time!" Megatron said.

Soundwave didn't say a word. Instead he replayed the scene where Megatron told Knock Out and Breakdown to go and not him. Megatron wide-opticed.

"Uh, well, when I said "you" I meant _all_ of you!" Megatron said. "You should come on out." Megatron added actually stepping into his room.

Soundwave wasn't used to Megatron coming towards him and backed up a bit.

"I'm not going to hurt you Soundwave! I'm just...concerned...a bit!" Megatron said rubbing the back of his head. If this was a non-CGI cartoon there would have been a sweat drop coming from the back of Soundwave's head while a big sweat drop would be coming from the back of Megatron's head.

Soundwave finally proceeded to step out of his room and walk with Megatron to the main control room to talk. Megatron may be a cruel and merciless leader but he would actually show concern for his TIC.

_**To be continued...**_


	3. Chapter 3: Close Calls

Chapter 3: Close Calls

_**Back at the Autobot Base...**_

Ratchet was alone, while he had a map of the island he was too bored to look at it. However, one thing was crowding his processor. What made "Thomas and Friends" so enjoyable? He decided to look it up. After about 20 minutes he was very surprised but not completely impressed. He prefered the models than the CGI. (I do too, those were the best!) He looked back at the TV to see "Thomas" was back on playing the old theme song. Ratchet hesitated to look but his optics were thinking otherwise. He began watching about 5 episodes from the model classic series.

"Not bad!" Ratchet said.

_**Meanwhile on the Nemesis...**_

Soundwave had dared Megatron to watch one episode, the pilot episode to be exact. Megatron was actually delighted to see that some of the engines had similarities to him. Gordon reminded him of himself while Thomas reminded him of Starscream.

**_Back on Sodor..._**

Starscream was over in the scrap yard trying to find energon. He only succeded in finding little bits of some. He thought he might as well use it up. After all he was very thirsty. Suddenly he heard an 2 engine whistles. It was Thomas and Henry. Starscream ducked behind a very large pile of scrap.

"Thanks for helping me out Henry!" Thomas said pushing some trucks into a siding.

"No problem!" Henry said pushing other trucks into another siding, then leaving.

Starscream took one step out accidently knocking another pile of scrap on the ground trapping Thomas.

"Cinders and ashes!" Thomas said surprised. "I'm trapped!"

Starscream face-palmed at his action. Now he was going to have to reveal himself to Thomas now instead of later. Starscream hoped Percy would have told him by now. Then he had an idea. He crept his way to behind Thomas. He carefully gripped Thomas' sides with his razor sharp claws and shoved him through the pile of scrap. Thomas was free but he was now confused. But before he could say anything a thought he heard a loud jet zoom overhead.

"That's strange." Thomas said looking up. He did not see Starscream at all. But what Starscream didn't know was that he had accidently left faded claw marks on Thomas' back.

Thomas went back to tidmoth sheds not really concerned with how he got out but instead was just glad he was. He saw Percy, Edward and a sleeping Emily at the sheds.

"Hello Percy, did you see the alien yet?" Thomas asked making Edward shutter.

"What's an alien?" Edward asked.

"I don't know! But Percy does right?" Thomas said looking at Percy who looked nervous.

"Uh Thomas that is something I should speak to you in private about." Percy said coming out of the shed towards the turntable where Thomas was.

"Mabye this is best saved for a better time." Percy quietly said.

"Please Percy, I want to see him!" Thomas pleaded.

"I don't know where he is!" Percy said. "Mabye he is still at the scrapyard." he added figuring out his idea.

Thomas and Percy headed back to the scrapyard to find no one there. Percy yelled out.

"ANYBODY HERE?" Percy yelled looking around. "I HAVE THOMAS WITH ME!"

"He's here?" a voice came back making Percy laugh.

"Yeah he wants to meet you!" Percy said. "Brace yourself Thomas." he added heading onto a track beside Thomas.

Starscream slowly stepped out from behind a pile of scrap scaring Thomas a bit. Thomas wide-eyed as Starscream walked towards him with a grin. Starscream bent down to Thomas' eye level getting a good look at him. Thomas stared at the glowing red optics, then at Percy, then back at Starscream.

"So you're the one Percy has been telling me about!" Starscream said.

"Y-y-yes! You have?" Thomas said looking at Percy who smiled bigger.

Starscream happened to look at Thomas' side and looked surprised when he saw that he had made claw marks on him.

"Thomas, I was the one who helped you out of that pile of scrap!" Starscream said pointing to where Thomas was trapped.

"Really? Thank you, I appreciate it!" Thomas smiled not feeling scared anymore.

"You know, how do you guys feel about...flying?" Starscream asked smirking.

"Well, I see why it's fun for people, but engines really don't like flying." Percy said.

"Come on! I'm sure _I _could make your disliking of flying change." Starscream said with a little evil tone in his voice.

Next thing Thomas and Percy knew they were being dragged around in the sky by Starscream and his grappling hook. Thomas and Percy were having a blast. They flew past Harold who did a double-take thinking he did not see what he just saw. Starscream flew them high enough to make sure no engine could see them. After about 5 minutes they landed back at the scrap yard. The trio laughed.

"That was actually fun!" Percy said.

"I know!" Thomas said.

"It was!" Starscream said. "Hey, shouldn't you guys be heading back to your sheds in case of a task?"

"Hey you're right!" Percy said.

"Thanks for the ride, it was fun!" Thomas said as he and Percy left the scrapyard. Starscream laughed.

"Nice guys!" Starscream said.

Meanwhile, Breakdown had found Knock Out by the seaside hiding from the humans. Knock Out was observing the beach.

"Knock Out?" Breakdown said coming over to the happy mech.

"Oh hey Breakdown like the view?" Knock Out asked not even looking at him.

"Dude, we are not here for sight-seeing, we are here for energon and that's it!" Breakdown snapped making Knock Out turn right towards him.

"YOU'RE NOT THE BOSS OF ME!" Knock Out snapped back.

"WELL YOU NEED TO DO YOUR JOB!" Breakdown snapped back again.

Both mechs gave each a long stare before Knock Out gritted his teeth.

"I WILL DO WHATEVER I WANT! GO AWAY!" Knock Out snapped causing Breakdown to grit his teeth too.

Knock Out turned away from him. In response, Breakdown grabbed a big ball of sand and threw it at Knock Out. Knock Out gasped at first then growled loudly and turned right back around.

"OH NO YOU DIDN'T!"

"OH I SO DID!"

"YOU WANNA GO?"

"BRING IT ON!"

Knock Out lunged at Breakdown and both began a brawl right in front of an abandoned boat that was once Bulstrode. Sand flew everywhere as both mech's kept at it. What they didn't realize was that Team Prime was nearbye spying around at the beach. Bee was the first to notice them. He buzzed wildly and pointed at the brawlers.

"Decepticons!" Arcee growled.

"Autobots! Dive in!" Optimus commanded as they begin shooting at the two mech's. Breakdown was just about to lay in another punch when he saw the Autobots.

"Autobots!" Breakdown growled.

"GET THEM!" Knock Out said charging them.

"YOU IDIOT TWO AGAINST FOUR?" Breakdown yelled as he transformed and fled.

"UGH!" Knock Out yelled at ran after Breakdown.

Team Prime quickly transformed and raced away. Just in time as James was rolling by enjoying himself.

"That was too close!" Bulkhead said.

"Tell me about it!" Arcee said.

"We will acomplish our goal team, it will just take time! But for now, we should find some place to rest!" Optimus said.

"But where? Anywhere we go there will probably be an engine!" Arcee said.

Bee buzzed an idea.

"The scrapyard...ew!" Bulkhead said.

"It's the only place!" Arcee said.

"It will have to do...SCRAP!" Optimus said screeching to a stop.

"What's wrong?" Bulkhead said.

"We forgot the kids at the beach!" Optimus said feeling embarrased.

_**NOTE: Readers, I would advise you to face-palm again since the Autobots actually forgot something important!**_

_**Meanwhile on the Nemesis...**_

Megatron was in the control room. He needed a new SIC since Starscream was gone. He thought back to watching "Thomas" with Soundwave. Suddenly, he had an evil plan!

"While my last SIC is gone, I believe I just found a new one!" Megatron said evily while a picture of Thomas appeared on the screen.

Little did he know, Soundwave was watching him from nearbye. If Soundwave had optics, they would have made him look very worried. Usually Soundwave did talk when no one knew he was there. So, Soundwave finally spoke.

"What have I done?"

**_To be continued..._**


	4. Chapter 4: Trainnapped

Chapter 4: Train-napped

_**On the Nemesis...**_

That night, a dented and angry Breakdown and Knock Out came through the groundbridge carrying more energon. They were not talking to each other. Megatron laughed when he heard about their little scuffle. But also a little angry as they could have blown their cover. As the two angry mechs walked to their own rooms, which were surprisingly right next to each other, they looked at each other, gritted their teeth, and walked right into their rooms without a word. Soundwave meanwhile saw the whole thing and so did a few eradicons. Soundwave however, was still thinking about Megatron's plan. What did he want with Thomas?

_**Back at the Autobot Base...**_

Ratchet was about to go to recharge when he recieved a call from Optimus. Ratchet had been alone the whole day and was relieved to hear from someone.

"Yes Optimus?"

"Do you know the locations of Breakdown and Knock Out?"

"Let me see...nope, nowhere in the island."

"We are going to remain here for the night. Recharge well old friend."

"Thanks Optimus, you too!"

Ratchet hung up and went straight to recharge.

_**Meanwhile on Sodor...**_

The autobots were taking turns watching for any signs of decepticons. Starscream was still sneaking around the island trying to find someplace to sleep. He flew around nearly half the island when he spotted a small shed. He transformed and peered in. It was revealed to be Toby's shed. He nearly fell in surprise when he saw Toby. Sadly he was too big for it. So he decided to fly over to the smelters yard. Luckily there was no one there so he decided to stay there, despite how hot it was. The next day, the Autobots began searching again.

_**Back on the Nemesis...**_

Megatron had finally thought of the whole plan. He decided not to tell Soundwave who already knew. He began to put his plan into motion.

"Breakdown to the control center now!" Megatron announced on a few speakers. Breakdown, still a little asleep, came in.

"Yes..*yawn*...Lord Megatron?" Breakdown asked.

Megatron's evil grin scared Breakdown completely awake.

"I need you to round up a few drones and go back to the island." Megatron began.

"Why sir?"

"I need you to capture...HIM!" Megatron pointed at a picture of Thomas that appeared on the screen.

Breakdown gave the picture a long stare before looking back at Megatron.

"Yes sir...but wait, pardon me, but you're not going to _kill _him are you?" Breakdown asked a little worried.

Megatron stepped right up to Breakdown's face making Breakdown wince a bit.

"If he doesn't do what I say. Oh and why you are there, bring me a big pile of track!" Megatron said with his grin getting bigger.

The groundbridge activated and Breakdown and 6 eradicons ran through. Megatron realized Knock Out and Soundwave were the only ones left. Knock Out was writing in his diary how much he wanted to pound Breakdown right now and Soundwave was thinking of a way to stop Megatron.

_**Back on Sodor...**_

Breakdown's mission was to locate Thomas and lure him towards the groundbridge. Breakdown had recieved coordinates of Thomas' location, the docks. As Breakdown entered the location, he found it was going to be pretty tough. Thomas, Cranky, Gordon and Percy were there. But Thomas was settled in a place Breakdown could probably go to lure him. Breakdown slowly rolled along the road. He went past Percy who was shunting trucks. Then Gordon who was waiting for passengers to aboard. And Thomas who had Annie and Clarabel with him talking to Cranky. Breakdown sped up to the side of Thomas and nudged him causing Thomas to look at him.

"Cinders and Ashes watch out!" Thomas said surprised.

Breakdown turned around to face Thomas then jumped on the tracks.

"I heard that you are interested in aliens. I believe I have seen more!" Breakdown said.

Thomas wasn't sure if he was an alien or a mysterious newcomer. But he did want to see more!

"Follow me!" Breakdown said backing up on the tracks.

Thomas was worried if he should go. In the end, he left Annie and Clarabel and followed Breakdown. They rolled around a corner away from the other engines. Suddenly Thomas gasped. There in front of him was a green swirl which was actually a groundbridge. Thomas just stared at it. Then Breakdown laughed evily.

"Pretty clumsy of you to actually follow me Thomas!" Breakdown said.

"Huh? I don't understand!" Thomas said.

Thomas was so confused he didn't notice the eradicons beggining to circle him. Breakdown then transformed right in front of Thomas' eyes. Thomas backed up in surprisement.

"AAH! WHO ARE YOU?" Thomas asked in a shock.

"YOU WILL KNOW SOON ENOUGH!" Breakdown said staring down the little tank engine.

Thomas then found himself surrounded by the drones.

"YOU'RE COMING WITH US!" Breakdown demanded changing his right hand into a hammer.

Thomas was too horrified to remember to whistle or yell. He found himself being pushed closer and closer to the groundbridge. What the decepitcons didn't know was that Bee was watching the whole time. Bee buzzed in disbelief. He raced to find the others.

_**On the Nemesis...**_

Megatron, Knock Out and Soundwave waited as the groundbridge revealed many figures. Breakdown entered first giving Knock Out "the finger" then stood in front of Megatron.

"Mission accomplished Sir." Breakdown said.

Thomas soon came through screeching his wheels on the metal of the Nemesis because there were no rails. A few of the eradicons had gathered rails. Thomas looked around. Robots, metal, darkness was all he could see. Thomas was speechless when he saw Knock Out, Soundwave and more eradicons. Megatron stepped in front of the scared tank engine who looked up at the towering mech.

"Thomas the tank engine...we finally meet!" Megatron said lowering his optics to Thomas' eye level.

"H-H-how do you-" Thomas was cut off by Megatron placing a sharp digit on Thomas' mouth.

"We do a little...research!" Megatron said grinning evily.

"What do you want from me?" Thomas asked seeing Knock Out and Soundwave walk closer.

Soundwave couldn't believe it, the star of one of his favorite shows, was on the Nemesis. He knew he had to help Thomas get home though.

"My SIC is gone, so I've arranged that _you_ will be my new SIC." Megatron said.

Thomas gulped. SIC to him sounded dangerous.

"We plan on salvaging some of your parts. And make you into a transformer like us!" Knock Out said coming closer.

Thomas didn't even know what that was! But apparently they were one of them and so was Starscream. Thomas looked down.

"But I can't move."

"Which is why we brought tracks to stretch around the whole ship." Breakdown said.

"SHIP?" Thomas said now looking around panicking.

"Oh, and I would strongly advise you to accept your fate because if you don't..." Megatron charged up his fuison cannon. "Your death will surely come." he finshed.

Thomas realized he was doomed but thought about asking a few questions.

"So...what is exactly is going on?" he asked.

_**Back on Sodor...**_

"THEY DID WHAT?" Miko yelled in horror.

"DARN CONS" Arcee yelled.

"THEY WILL PAY!" Bulkhead yelled.

"Autobots, we must abandon the search for Starscream and rescue Thomas. However, they have possibly revealed what was going on. So, we must give up our cover!" Optimus said, much to the dissapointment of the others.

And so the rescue of Thomas began. Optimus and the team went to Tidmoth Sheds. Little did they know, Starscream was watching the whole time. He gulped realizing his lies have came back to haunt him. Meanwhile Soundwave was getting ready to plan a rescue mission of his own. Suddenly Soundwave had an idea. He decided to journey to the Island of Sodor to join the Autobots and also confront a certain seeker.

_**To be continued...**_


	5. Chapter 5: Operation Thomas Pt1

Chapter 5: Operation Thomas Pt.1

_**On the Nemesis...**_

About an hour later, the decepticons had changed Thomas' look. Thomas was painted purple with red stripes. The number one on his sides were replaced with the decepticon insignia painted on his sides. He also got his whistle taken off because Megatron thought it was annoying. Thomas rolled around the Nemesis feeling confused and afraid. Many eradicons looked at him. He looked at back seeing that they had no mouth or regular eyes. Thomas barely said a word. Meanwhile Soundwave was putting his plan to action. He just needed to find Thomas himself. Thomas was quickly adjusting to the new tracks but was still very frightened. Breakdown passed by him smacking him lightly on the forehead. Soundwave finally found him going down one hallway.

"Hey...hey Thomas...over here!" Soundwave said actually speaking.

Thomas stopped to see the faceless con.

"I'm going to help you out!" Soundwave whispered coming over to meet face-to-face with him.

"Why?" Thomas whispered back.

"I never wanted him to do this, you don't deserve to suffer. After doing something like this, I am done with serving Megatron. So, I am on your side now." Soundwave whispered.

This made Thomas happy. Suddenly an eradicon came running towards them.

"Hey, can I go with you?" ST-3-VE said.

Soundwave responded by using recordings. He had one from a few days ago.

_"Why should I do that?"_ the recording of Megatron boomed from the faceplate screen.

"I am a fan too!" ST-3-VE whispered to Soundwave. In response Soundwave gave a thumbs up.

"I wish I had my whistle." Thomas said sadly.

"You mean this?" ST-3-VE said holding it out! "I found it!"

Thomas was very happy as it got it put back on.

"So how are we doing this?" Thomas asked.

"I was going to activate a groundbridge for you but Megatron would realize you're gone and probably destory the whole island so I need to go myself so I can get the Autobots to cause a big distraction. Then I will come back for you." Soundwave explained.

So, Soundwave activated a groundbridge and went through leaving Thomas and ST-3-VE behind.

_**At the Autobot Base...**_

Ratchet recived an urgent call from Optimus.

"Yes Optimus?"

"Ratchet...we have to blow our cover." Optimus said sounding sad.

"But Optimus-"

"Don't worry, I'm sure they will understand. We must have you here too!" Optimus said.

"Alright, I'm on my way!" Ratchet sighed and ended the call.

_**On sodor...**_

Ratchet groundbridged himself behind Tidmoth Sheds. There, the team and humans were already there. Just then, STH arrived.

"That's are cue." Arcee said.

The team headed straight for the front of the sheds surprising STH and all the engines including Toby. They transformed and recieved huge eyes. STH and his two men (the ones who stand behind him) gasped. Gordon was comepletely amazed. Percy smiled. Edward, Emily and Toby were scared. Henry backed up a bit causing Optimus to hold out his hand.

"Don't worry, we come in peace from another planet." Optimus said.

Miko, Jack and Raf were amazed to meet the engines face-to-face. Then Optimus began to explain the entire Cybertronian situation, and the missing Starscream.

"Hey, I saw Starscream!" Percy said. "He's a good friend."

"Should we tell him that his "friend" is evil?" Bulkhead whispered to Optimus.

"No, let's not make him sad." Optimus whispered back.

Meanwhile over inside the smelters yard, Starscream was looking around for more energon. What he didn't know was that Soundwave was looking for him around there. Starscream just happen to look back from where he started only to turn back around to stare right at Soundwave. Starscream fell back in surprise.

"SOUNDWAVE? WHAT ARE YOU DOING HERE?" Starscream yelled both scared and angry.

Soundwave didn't have time to play any recordings so he spoke instead.

"I need you to help me rescue Thomas!" Soundwave said surprising Starscream.

"Rescue Thomas? What happened?"

"He got captured by Megatron!" Soundwave said.

"I'm not going back there. Megatron will kill me!"

"You don't have to go to the Nemesis, but instead, be a look-out when the Autobots go to rescue him." Soundwave said getting angry.

"Like _I_ would help the Autobots." Starscream said crossing his arms.

Soundwave lost it, he shoved Starscream into a wall hard. Starscream wanted to fight back but Soundwave had his hands pinned to the wall.

"LISTEN UP, I AIN'T GOT A LOT OF TIME, EITHER YOU HELP ME OR YOU WILL DIE RIGHT WHERE YOU ARE AT!" Soundwave yelled right in Starscream's horrified face.

"ALRIGHT ALRIGHT I'LL HELP!" Starscream yelled back.

Soundwave let go and backed off.

"Besides, I quit too!" Soundwave said recieving a smirk from Starscream.

"I always knew you would come around." Starscream said.

"Whatever, come on!" Soundwave said as both of them transformed and flew to Tidmoth Sheds.

Optimus had just got done describing the whole war which everyone was listening to. STH smiled.

"Well, Autobots, I suppose it is up to you to rescue Thomas." he said.

Percy began to tear up.

"Please bring him back." Percy said beggining to cry.

"Don't worry, we will" Optimus said.

Just then Starscream and Soundwave arrived. The Autobots drawed their weapons. Only to recieve one word.

"STOP" yelled Soundwave.

They transformed and looked at the autobots and engines. Arcee wanted to charge Starscream but Bee tried to hold her back.

"Looks like we-OW!" Bulkhead got slapped by Ratchet. "Oh yeah!" he said looking back making sure Percy didn't hear that.

"What do you want Soundwave?" Optimus said.

"I'm done with Megatron. Him kidnapping Thomas was one of the worst things he could possibly do. SCREW HIM!" Soundwave said.

"I'm helping!" Starscream said.

Optimus raised an optic-ridge.

"Are you sure this isn't some trick?" Bulkhead said.

"LISTEN WE DON'T HAVE TIME, WHO KNOWS WHAT MEGATRON IS DOING TO THOMAS!" Soundwave said flailing his arms in the air.

Optimus turned to the engines.

"You have my promise that Thomas will return here." Optimus said.

A groundbridge opened and all the mechs and femme went through. The groundbridge was teleporting them to the Nemesis. This left the other engines with their faces looking like they saw half the island explode. Now for the final objective. SAVE THOMAS THE TANK ENGINE!

**_To be continued..._**


	6. Chapter 6: Operation Thomas Pt2

Chapter 6: Operation Thomas Pt.2

_**On the Nemesis...**_

Thomas was in an abandoned room that used to belong to a random eradicon. He was thinking about Percy, Annie, Clarabel and his other friends. He thought about getting back home. Did he do the right thing to trust a robotic stranger? Suddenly a familiar voice boomed through the speakers on the walls.

"New SIC, I need you in the main control room." Megatron's voice boomed evily.

Thomas' lower lip quivered. He slowly rolled down the new tracks through a long hallway without a word. About 2 minutes later he arrived. Megatron was facing him with a evil grin. Thomas stopped inches before his feet and just stared at Megatron's optics.

"Have you seen Soundwave anywhere?" Megatron asked lowering to Thomas' eye level.

Thomas had to lie, if he gave up Soundwave's cover he would be in big trouble.

"No sir!" Thomas said. "Is he usually around here?"

"Yes, but I haven't seen him all day!" Megatron said.

"I'm sure he will turn out, he can't just leave." Thomas said. In his mind he was repeating the word "SCRAP!".

Megatron noticed Thomas didn't have anywhere to be grabbed by under his head so he grabbed Thomas under his buffers and lifted him up a bit with an angry stare.

"You better not be lying!" Megatron said taking his free servo and clawed the top of Thomas' head in front of his funnel. "If you are lying I shall rip you to a million pieces." Megatron threatened.

Thomas was very shocked. Megatron put him down on the tracks, but not gently. He pretty much dropped him as if he was a toy. Thomas backed away nearly running into a walking Knock Out.

"Hey watch it!" Knock Out said glaring at the engine.

"Sorry, I'm just a little surprised is all." Thomas said backing up some more to his room. "Where is Soundwave?" he thought to himself.

Speaking of Soundwave, he, Starscream, and Team Prime had just groundbridged to Soundwave's room. Soundwave contacted ST-3-VE to come over which he did.

"Now what?" Bulkhead said.

"What do you think? Find Thomas!" ST-3-VE said angrily.

"WATCH YOUR TONE 'CON!" Bee buzzed angrily.

"MAKE ME!" ST-3-VE snapped back before both were seperated by Starscream.

"Guys, less fighting more saving!" Starscream said. Then he remembered something. "Uh Soundwave were you serious about the killing me thing?"

"No, but I would have beaten you harder than Megatron ever did." Soundwave said. "Now then, me and ST-3-VE will distract Megatron and ask for location of Thomas while the rest of you...might have to fight the other drones, Breakdown and Knock Out." Soundwave explained. "Wait for our cue."

"Seems fair enough." Arcee said sarcastically receiving a glare from Soundwave.

"LET'S MOVE!" ST-3-VE said as they all ran in different directions.

Soundwave and ST-3-VE ran through the hallways looking for Megatron. They ran past other drones who were confused on what was going on. Some whispered to others. Luckily, Megatron was still in the main control room. He turned and grinned evily.

"Ah, Soundwave...and a drone." Megatron said. "Where have you been?"

"Uh...bathroom?" Soundwave said worried trying to make it not sound like he was lying.

"Really? The bathroom for 3 hours?" Megatron said in a light tone while stepping towards them.

"Yeah!" Soundwave said. "Energon got to me this time."

ST-3-VE felt like slapping Soundwave upside the head but he remained calm. Megatron backed off and turned around. But kept his head towards them.

"Well then, carry on!" Megatron said turning his head back and walking slowly towards a window.

"Escuse me sir?" ST-3-VE said nervously.

"Speak!"

"Where might Thomas' room be?"

"Why?"

"Me and some of the other drones wanted to...pick on him, make him feel weak!" ST-3-VE said while cursing himself in his head. Now Soundwave wanted to smack _him_ upside the head.

Megatron, without a word, showed a map on a screen revealing Thomas' location. The duo left. Meanwhile Team Prime had been causiously looking around. No drones in sight. They had left Raf, Miko and Jack on Sodor as it was too dangerous. As Soundwave and ST-3-VE found Thomas' room they looked to see if anybody else was around. No one was, so they crept in and they found Thomas sleeping.

"Thomas, THOMAS!" Soundwave whispered.

"Huh, what?" Thomas said finally awake but still very sleepy.

"Mission is nearly complete, let's move." ST-3-VE said excited.

Thomas grew a big happy face. Then Soundwave's faceplate screen showed fire meaning he had an very clever idea.

"Okay Thomas blow your whistle!" Soundwave said.

"Why?"

"Just do it, trust me!"

PEEP PEEP PEEEEEEP!

Everyone on the Nemesis heard it. Megatron heard and growled.

"THAT'S OUR CUE!" Bulkhead said.

Team Prime began charging down hallways to get to Thomas. Knock Out wasn't going to fight because he had just painted his paint job but he gave is electric prod to a drone. Breakdown charged the team with a few drones. Suddenly, Thomas rushes out from another hallway with Soundwave and ST-3-VE in his cab.

"YEEEEEEE-HAW!" Soundwave said. "THOMAS COMING THROUGH!"

Breakdown and the drones wide-opticed as Thomas actually bashed into them all. Bulkhead, Starscream and Bee laughed their afts off. They all kept crashing and bashing drones as they made their way to where Megatron was waiting with about 30 drones.

"Starscream got your grappling hook?"

"I always have it with me why?"

"Hook to Thomas, transform and hold on!" Soundwave said with Starscream figuring out the plan. Starscream latched it to Thomas and transformed. Soundwave transformed with and blasted down locked doors and more drones. Team Prime transformed too and raced down the hallways. Thomas was enjoying the ride as it felt nearly like the time he raced with the jet engine. They finally reached where Megatron was at. As the doors were blown off, many of the drones exploded along with the door. Megatron didn't have time to react as Thomas plowed him down. To add injury, Bulkhead and Optimus drove over him too but Megatron recovered fast.

"AUTOBOTS, THOMAS...SOUNDWAVE AND STARSCREAM YOU TRAITORS!" Megatron yelled and fired his fusion cannon.

Optimus transformed and blocked the blast with his sword. Soundwave, Starscream and ST-3-VE, who transformed, blasted the front end windows of the Nemesis. As they all jumped out of the Nemesis, Optimus quickly blasted Megatron twice with his guns. At this point, Starscream had uncoupled from Thomas. All of them were free falling from the Nemesis.

"AAAAAAAAHHHHHHHH!" Thomas yelled. He couldn't see the ground.

Soundwave, Starscream and ST-3-VE transformed to robot mode and were actually enjoying the fall.

"THIS IS NOT FUNNY!" Ratchet yelled.

"GROUNDBRIDGE US!" Arcee yelled.

"NOT COOL" Bee buzzed.

"SOUNDWAVE!" Bulkhead yelled.

"Ruin all the fun!" Soundwave said groaning.

But just as Soundwave was about to groundbridge them, Megatron caught up with them and began firing in his jet mode. Luckily all of them were far from hitting the ground. But Starscream latched back to Thomas to keep him safe.

"GET BACK HERE!" Megatron yelled still firing, mostly at Optimus who was also firing back.

"EVERYONE HOLD UP, I HAVE A SURPRISE!" ST-3-VE yelled at everyone who looked at him. "Thomas...whistle 5 times fast."

Thomas did quickly and suddenly two powerful fusion cannons came out of Thomas' cab. Starscream flipped Thomas around so he was facing Megatron. Everyone stared in shock. Thomas saw the guns and was too shocked to say a thing.

"THOMAS, WHISTLE ONCE FOR 5 SECONDS!" ST-3-VE yelled.

Thomas did and the fusion cannons fired twice and made a direct hit to Megatron who growled in pain. Megatron flew off course and ended up flying into a very tall rock formation finally defeated. Soundwave groundbridged them back to Sodor as they actually had to fall into the spiral of green.

_**On Sodor...**_

Raf, Miko and Jack waited for Team Prime to come back at Tidmoth Sheds. All the engines were there too worried for Thomas. Suddenly, a spiral of green appeared in front of everybody revealing the rescue team and Thomas. Everyone cheered and whooped.

"You're back!" Milko said excitedly.

"Hooray!" Raf said.

"Nice job!" Jack said.

"Thomas you're home!" Percy said and nearly cried.

"Hooray for the Autobots!" All the engines cheered.

"Thomas welcome home!" STH said happily.

"Thank you sir!" Thomas said.

"Wait, ST-3-VE, where did you actually get time to put in those guns?" Starscream asked the con he had bitch-slapped a very long time ago.

"I have my ways!" ST-3-VE said. "But now they have to be taken off."

He went to detach the guns from Thomas while recieving shocks from everybody. Starscream and Soundwave saw Percy.

"Starscream, what are you going to do now?" Percy asked puffing closer to him.

"Well I thought about mabye to continue to travel the world. But I will be back." Starscream said putting a smile on his face.

"Yeah, we will too!" Soundwave said. ST-3-VE nodded.

"You two actually want to tag along with me?" Starscream asked looking puzzled.

"Sure, us seekers need to stick together!" ST-3-VE said.

"Thank you so much Autobots, I owe you!" Thomas said happily.

"Don't worry Thomas, you're help was enough, but we will help you get back to normal." Optimus smiled.

_**A few days later...**_

_**Optimus' thought...**_

_"We had experienced a nice island full of interesting machines. We have made new friends and possibly new allies. We owe them our life for their help in saving their own kind. We plan on returning one day, mabye for what the humans call, a vacation. We don't have any clue as to where Soundwave, Starscream or the drone have gone. But we now see them as our friends...mabye not with Arcee. But, until we meet with the engines again, we left a little present behind..."_

_**In reality...**_

Thomas is seen with Annie and Clarabel on the bridge like in the original intro about to past by the windmill. Thomas is back to his original paintwork with the number 1 on his sides. He also had a new feature. An Autobot insignia branded on the front of his funnel.

_**The End...**_

_**I had a lot of fun making this. I really want to know what you guys think but no bad comments. I consider this a good ending. Didn't come out as awesome as I hoped but I can live with this! So, until my next Transformers Prime story. I'M OUT...PEACE!**_


End file.
